Ireland has one of the oldest systems of patrilineal hereditary surnames in the world. Using the paternal co-inheritance of Y-chromosome DNA and Irish surnames, we examined the extent to which modern surname groups share a common male-line ancestor and the general applicability of Y-chromosomes in uncovering surname origins and histories. DNA samples were collected from 1,125 men, bearing 43 different surnames, and each was genotyped for 17 Y-chromosome short tandem repeat (STR) loci. A highly significant proportion of the observed Y-chromosome diversity was found between surnames demonstrating their demarcation of real and recent patrilineal kinship. On average, a man has a 30-fold increased chance of sharing a 17 STR Y-chromosome haplotype with another man of the same surname but the extent of congruence between the surname and haplotype varies widely between surnames and we attributed this to differences in the number of early founders. Some surnames such as O'Sullivan and Ryan have a single major ancestor, whereas others like Murphy and Kelly have numerous founders probably explaining their high frequency today. Notwithstanding differences in their early origins, all surnames have been extensively affected by later male introgession. None examined showed more than about half of current bearers still descended from one original founder indicating dynamic and continuously evolving kinship groupings. Precisely because of this otherwise cryptic complexity there is a substantial role for the Y-chromosome and a molecular genealogical approach to complement and expand existing sources.